We will apply next-generation sequencing (NGS) technology to assess the genome-wide pattern of structural variation within large (>20 kbp), complex regions of segmental duplication. Combining read-depth and a single-base unique nucleotide (SUN) identifier map, we will generate absolute estimates of diploid copy-number and sequence content for duplicated regions and gene families. We propose to analyze all 2,000 individuals being analyzed as part of the 1000 Genomes Project and to validate regions by a combination of array comparative genomic hybridization (arrayCGH), clone-based sequencing and FISH-based approaches. This aim will provide the first genotypic assessment of copy and content of these complex regions facilitating future disease association studies.